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The effect of time-ordered-expression (TOE) mRNA vaccination on the expression of immune-related genes during the activation and maturation of BMDCs

GSE279604 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/10/16 Platform GPL28330
At a glance

RNA-seq (gene expression) · mouse · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
18 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
The adjuvant translational control plays a pivotal role in shaping immune responses,which means that precise kinetic modulation of mRNA vaccines could help to elicit stronger immune responses.Here, we constructed lipid nanoparticles (LNPs) encapsulating the TOE mRNA(OVA-IL-12) encoding OVA (normal expression) and IL-12 (delayed expression), and also constructed LNPs encapsulating a mRNA simultaneously expressing OVA and IL-12 (OVAoIL-12), LNPs encapsulating mRNAs expressing
Read the full summary ↓
OVA or IL-12 individually, and LNPs encapsulating equimolar mixtures of mRNAs encoding OVA and IL-12 (OVApIL-12) as control groups.we demonstrated that the TOE mRNA kept the activation of the mTORC1 pathway, as characterized by increased expression levels of crucial genes such as Tsc1, Pik3ca, and Eif4ebp1, which potentially contributed to the improved antigen expression in the cells.We also evaluated the overall transcriptome change after LNP transfection via RNA-seq and found that TOE mRNA transfection also markedly upregulated key genes associated with immune activation.Taken together,our study introduces a transformative platform for mRNA vaccine design that could overcome the limitations of conventional mRNA vaccines. By precisely controlling the time course of adjuvant translation, this new platform enhances vaccine efficacy without compromising safety, opening new avenues for the development of advanced therapeutic and prophylactic interventions.
This dataset
Open GSE279604 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE279604_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1173588 and SRA study SRP538917. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
BMDC,ctrl,24h , ×3 BMDC,IL12,24h , ×3 BMDC,OVA-IL12,24h , ×3 BMDC,OVA,24h , ×3 BMDC,OVAoIL12,24h , ×3 BMDC,OVApIL12l,24h , ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.